Detailed Information

HH-suite3 for fast remote homology detection and deep protein annotation

Cited 491 time in Web of Science Cited 505 time in Scopus

Steinegger, Martin; Meier, Markus; Mirdita, Milot; Voehringer, Harald; Haunsberger, Stephan J.; Soeding, Johannes

Issue Date
BioMed Central
BMC Bioinformatics, Vol.20 No.1, p. 473
Background: HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous proteins. Results: We developed a single-instruction multiple-data (SIMD) vectorized implementation of the Viterbi algorithm for profile HMM alignment and introduced various other speed-ups. These accelerated the search methods HHsearch by a factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is similar to 10x faster than PSI-BLAST and similar to 20x faster than HMMER3. Jobs to perform HHsearch and HHblits searches with many query profile HMMs can be parallelized over cores and over cluster servers using OpenMP and message passing interface (MPI). The free, open-source, GPLv3-licensed software is available at Conclusion: The added functionalities and increased speed of HHsearch and HHblits should facilitate their use in large-scale protein structure and function prediction, e.g. in metagenomics and genomics projects.
Files in This Item:
There are no files associated with this item.
Appears in Collections:

Related Researcher

  • College of Natural Sciences
  • School of Biological Sciences
Research Area Development of algorithms to search, cluster and assemble sequence data, Metagenomic analysis, Pathogen detection in sequencing data


Item View & Download Count

  • mendeley

Items in S-Space are protected by copyright, with all rights reserved, unless otherwise indicated.